Cellects, a software to quantify cell expansion and motion

Abstract

MotivationGrowth and motion quantification is a crucial step in studying the evolution, growth and behavior of many species. However, there is no free and easy to use software to automatically quantify the growth of an organism, and that works across a wide range of species. To fill this gap, we developed Cellects, an open-source software that quantifies growth and motion under any conditions and for any species.SummaryAutomated quantification offers unique opportunities to study biological phenomena, increasing reproducibility, replicability, accuracy, and throughput, while reducing observer biases. We present Cellects, a tool to quantify growth and motion in 2D. This software operates with image sequences containing specimens growing and moving on an immobile flat surface. Its user-friendly interface makes it easy to adjust the quantification parameters to cover a wide range of species and conditions, and includes tools to validate the results and correct mistakes if necessary. The software provides the region covered by the specimens at each point of time, as well as many geometrical descriptors that characterize it. We validated Cellects withPhysarum polycephalum, which is particularly difficult to detect because of its complex shape and internal heterogeneity. This validation covered five different conditions with different background and lighting, and found Cellects to be highly accurate in all cases. Cellects’ main strengths are its broad scope of action, automated computation of a variety of geometrical descriptors, easy installation and user-friendly interface.github link:https://github.com/Aurele-B/CellectsHighlightsWe present Cellects, a tool to quantify growth and motion of organisms automatically.Cellects is easy to install and use thanks to its user-friendly interface.It works with a wide range of organisms, providing many geometrical descriptors.Our validation showed high accuracy even in challenging experimental conditions.